Transposon control as a checkpoint during regeneration

转座子控制作为再生过程中的检查点

• 批准号: 10607420
• 负责人: Krista Marie Angileri
• 金额: $ 7.18万
• 依托单位: CORNELL UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-12-01 至 2026-11-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10607420
• 关键词: Ablation; Affect; Animals; Biological Assay; Cells; Chemicals; Chromatin; Complex; Cone; DNA Damage; DNA Transposable Elements; Data; Data Set; Defect; Development; Elements; Environment; Eukaryota; Eye; Family; Foundations; Gene Expression Profile; Genetic; Genome; Genomics; Gonadal structure; Homeostasis; Human; Inflammation; Inflammatory; Inflammatory Response; Injury; Mediating; Mobile Genetic Elements; Modeling; Molecular; Mus; Natural regeneration; Neurons; Nucleic Acids; Organism; Outcome; Pathway interactions; Pattern; Photoreceptors; Planarians; Process; Proliferating; Proteins; Recovery; Recovery of Function; Regenerative Medicine; Regenerative capacity; Regulation; Reporting; Repression; Resolution; Retina; Role; Salamander; Sea Cucumbers; Specificity; Structure; Study models; System; Testing; Time; Tissue-Specific Gene Expression; Tissues; Up-Regulation; Urochordata; Variant; Work; Zebrafish; cell type; comparative; experimental study; eye regeneration; functional restoration; genetic analysis; genome integrity; improved; in vivo; inhibitor; injured; insight; model organism; multimodality; multiple omics; mutant; novel; pharmacologic; regenerative; regenerative therapy; response to injury; retinal neuron; retinal regeneration; single-cell RNA sequencing; stem cell self renewal; stem cells; timeline; tissue injury; tissue regeneration; tissue repair; transcriptome sequencing; transcriptomics; transposon/insertion element; Ablation; Affect; Animals; Biological Assay; Cells; Chemicals; Chromatin; Complex; Cone; DNA Damage; DNA Transposable Elements; Data; Data Set; Defect; Development; Elements; Environment; Eukaryota; Eye; Family; Foundations; Gene Expression Profile; Genetic; Genome; Genomics; Gonadal structure; Homeostasis; Human; Inflammation; Inflammatory; Inflammatory Response; Injury; Mediating; Mobile Genetic Elements; Modeling; Molecular; Mus; Natural regeneration; Neurons; Nucleic Acids; Organism; Outcome; Pathway interactions; Pattern; Photoreceptors; Planarians; Process; Proliferating; Proteins; Recovery; Recovery of Function; Regenerative Medicine; Regenerative capacity; Regulation; Reporting; Repression; Resolution; Retina; Role; Salamander; Sea Cucumbers; Specificity; Structure; Study models; System; Testing; Time; Tissue-Specific Gene Expression; Tissues; Up-Regulation; Urochordata; Variant; Work; Zebrafish; cell type; comparative; experimental study; eye regeneration; functional restoration; genetic analysis; genome integrity; improved; in vivo; inhibitor; injured; insight; model organism; multimodality; multiple omics; mutant; novel; pharmacologic; regenerative; regenerative therapy; response to injury; retinal neuron; retinal regeneration; single-cell RNA sequencing; stem cell self renewal; stem cells; timeline; tissue injury; tissue regeneration; tissue repair; transcriptome sequencing; transcriptomics; transposon/insertion element

PROJECT SUMMARY / ABSTRACT Tissue regeneration is the process through which damaged tissue is restored to its original structure and function. There is wide variation across species in their regenerative ability. For example, zebrafish can regenerate all retinal neurons after injury while humans and mice cannot. Understanding the genetic basis and molecular underpinnings of complex tissue regeneration in model species holds the promise to enhance human regenerative medicine. Here I am using zebrafish to test the novel hypothesis that the control of transposable elements (TEs) is a necessary checkpoint for complex tissue regeneration. TEs are mobile DNA elements capable of self-replication that are ubiquitous and abundant in eukaryotes. Uncontrolled TE activity leads to accumulation of TE-encoded nucleic acids and proteins that interfere with cell homeostasis and can result in DNA damage, disrupting genome integrity. TE upregulation has been reported during tissue regeneration in salamanders, sea cucumbers, and worms. I hypothesize that TE activation is a hallmark of tissue injury that must be suppressed for successful regeneration, and an inability to suppress TEs will stall regeneration. Supporting this hypothesis, my preliminary analyses of bulk RNA-seq data reveal TE upregulation during early stages of eye regeneration that are later restored to control levels prior to tissue repair. I predict that zebrafish and other organisms with a strong regenerative capacity deploy specific control systems to suppress TE activity during regeneration. Here I will directly test the role of the Piwi pathway in suppressing TE activity during zebrafish eye regeneration. The Piwi pathway is known to repress TEs in animal gonads, including zebrafish, but there is growing evidence that the pathway is active in somatic tissues and required for regeneration in planarians. Furthermore, I have detected piwil1 expression in the zebrafish eye, raising the testable hypothesis that it functions during eye regeneration. I will utilize a model of zebrafish retinal regeneration and a 2-pronged approach combining multimodal genomics and manipulative experimentation. First, I will further establish that TE upregulation is a hallmark of tissue injury by profiling TE expression changes across five regenerating tissues using publicly available single- cell transcriptomic data. Second, I will generate a multi-omic single-cell dataset to assess TE expression changes during cone regeneration from the onset of injury through to functional recovery. These data will provide the most comprehensive and precise view of TE expression dynamics during regeneration for any species. Lastly, I will directly test whether TE repression is required for regeneration by modulating TE activity using Piwi pathway mutants and chemical inhibitors of TE activity. Together the outcomes of this project will be the first to directly assess the role of TE activity and regulation during complex tissue regeneration. Moreover, these studies will lay the foundation for new testable hypotheses surrounding differences between regeneratively competent versus incompetent organisms and lead to the development of novel regenerative therapies.

项目摘要 /摘要 组织再生是将受损组织恢复到其原始结构和 功能。物种的再生能力之间存在很大差异。例如，斑马鱼可以 受伤后的所有视网膜神经元再生，而人类和小鼠不能。了解遗传基础和 模型物种中复杂组织再生的分子基础有望增强人类 再生医学。在这里，我正在使用斑马鱼来检验可转移的控制的新假设 元素（TES）是复杂组织再生的必要检查点。 TES是能够自我复制的移动DNA元素，这些元素在真核生物中无处不在且丰富。 不受控制的TE活性导致干扰细胞的Te核酸和蛋白质的积累 稳态并可能导致DNA损伤，从而破坏基因组完整性。据报道 在萨拉曼，海参和蠕虫的组织再生过程中。我假设激活是 必须抑制成功再生的组织损伤的标志，并且无法抑制TES 会失速再生。支持这一假设，我对散装RNA-seq数据的初步分析揭示了 眼睛再生的早期阶段的上调后来恢复到组织修复之前的控制水平。 我预测斑马鱼和其他具有强大再生能力部署特定控制系统的生物 抑制在再生过程中的TE活动。在这里，我将直接测试PIWI途径在抑制中的作用 斑马鱼眼再生期间的活性。已知Piwi途径会在动物性腺中压制TES， 包括斑马鱼，但有越来越多的证据表明该途径在体细胞中是活性的，并且需要 平面主义者的再生。此外，我在斑马鱼眼中检测到了piwil1的表达，提高了 可检验的假设，即它在眼睛再生过程中起作用。 我将利用斑马鱼视网膜再生模型和一种结合多模式的2条方法 基因组学和操纵实验。首先，我将进一步确定TE上调是 通过分析TE表达在五个再生组织中的表达变化，使用公开可用的单一单一的单个单一的损伤 细胞转录数据。其次，我将生成一个多摩尼克单细胞数据集来评估TE表达式更改 从损伤开始到功能恢复期间的锥体再生期间。这些数据将提供最多的 任何物种再生过程中TE表达动力学的全面和精确的视图。最后，我会的 直接测试是否需要使用PIWI途径调节TE活动，是否需要TE抑制 TE活性的突变体和化学抑制剂。该项目的结果将是第一个直接的 评估TE活性和调节在复杂组织再生中的作用。而且，这些研究将 为新的可再生能力差异的新可检验假设奠定了基础 与无能的生物相对于无能的生物，导致了新型再生疗法的发展。